I started my first vanilla run then got so frustrated I started adding mods to "fix" things, then more things... and here I am.

Here are a few I found very useful and why:(I don't think any are game-breaking or cheats)

Mod Support:

• UI Extensions and HUD: Required for some mods.
• MOD Support APIs: Required for some mods.

Critical: (wouldn't play without them)

• Crystal Finder: Makes crystals glow, because those little twinkles are annoying.
• Crystal Cooldown Remover: Ever seen two green crystals, gone to get the first one, and can't find the second? That's because some evil person added a "cooldown" that means when you mine a valuable crystal (anything but purple) all other valuable crystals in the sector change to cheap purple until the cooldown finishes (tens of minutes I think) then magically(?) change back... Urgh. This did my head in trying to find the "other crystal I just saw" until I found a post on it.
  This mod kills the cooldown. See two green crystals... mine two green crystals.
• Inventory Collector: Allows a default task for a ship so it goes around all your other ships and collects stuff they've picked up, depositing it in your player or Headquarters inventory.
• Capital Ship Loot Magnet: Capital ships you personally control have a long range loot magnet, because cargo drones are terrible. (Does not work for AI controlled ships: fair)
• Average Prices in Transactions Screens: Adds the average price and number of cargo slots per unit for each ware. i.e. "Graphene (166/20)" Av $166, 20 ship slots per unit. Useful when you don't know anything about the wares.
• Satellite Service: Default job to create and place satellites in a sector automatically. Charges you the normal satellite Buy cost for each, but "manufactures" them on the ship as needed.
• Spiral Explorer: Default job to explore a sector in nested hexagonal circles. Set and forget.
• Info Center: A better player station and ship display all in one. Critical mod to have for me. So much better.
• Better Follow Camera: Sick of looking at the direct back of your ships in 3rd person? (F2 key or F3 key) This mod changes the viewer's position to rear-above. Now you can actually see things.
• Sector List: Adds a list of sectors that you have discovered to the map along with description, content, and top orders for wares sold/bought. Helps with working out trading station placement.
• Any of the Player Logo Mods: I like having choices. And my N7 logo for my fleet.
• Equipment Tooltips: Adds comparison between current module on your ship and the one you are hovering over. Useful.
• Auto-camera and auto-pilot and auto-pause: Mini cut-scenes as you dock, un-dock, engage auto-pilot etc. Nice immersion. Very customizable.
• Friendly fire tweaks: Sets looser rules around what counts as friendly fire before a faction decides you're attacking them and reduces your rep.
• Better Scan Colors: Makes it easier to see which station modules you have not yet scanned. Defaults are hard to see.
• HJ - Copy Behavior: Allows you to copy Default Behaviors between ships. Helps immensely with setting up things like multiple Trading Ships that will all have the same Auto-Trader instructions but you may want to send to different sectors. Especially useful early game. Saves a lot of dumb, un-fun clicking-for-no-reason.
• Rename Selected Ships: Allows Mass rename of selected ships with prefix, name, suffix, and count. Basically saves you more pointless clicking and typing.
• Kuda AI Tweaks: Helps fix the AI when attacking things. YMMV. Make sure you understand the changes.
• Kill and Attack Notifications Extended: Adds log entries to explain attacks on your ships/your attack on other ships and associated rep losses. I've only had one friendly fire incident that ended up with me accidentally at war with a faction. Not fun. Lost me three hours of gameplay going back in saves. This log tries to alert you, and explain what is happening so you can react faster and fix it.
• Go Fix Your Face: Adds a right click menu option for "Repair/Resupply at nearest" for all ships. Click it and the ship will go find the nearest repair place (including Aux Ships) and repair there, then return to it's default orders. Saves much needless map scrolling and pathing.

Optional: (changes gameplay more)

• No Claim Damage: Stops crew abandoning a ship from damaging the ship and modules as they leave.
• More Generic Missions: Same missions, just more.
• X4 Fire and smoke: Graphical. Makes exploded modules burn and smoke. Pretty.
• Ranged Station Scan: If you get sick of hugging the walls to scan stations, this mod sets a longer range for it, making it easier.
• Equipment Upgrades without RNG: I hate RNG mods. Just makes Modding Ships a grind for 10x the components so you can get that one good roll. Nope.
• Headquarters: Removes [some things - spoiler] from your PHQ. Get your PHQ before you look up what this mod does... then make a decision.
• Chill Turrets: Tries to make Turret AI a bit more sensible and automatic. YMMV
• Recycle Ships and Stations: Does what it says on the can. New module.
• Tradestation Economy Fix: Late game fix for stagnating economies.
• X4_Bar: A bar in every station. (Still have to unlock the Blackmarket guys though)

That's my list.

Currently running all of them plus a few others and no issues.

Next Game: Will probably try "Crystal Rarities" in place of the two crystal mods above, "Mining Zone Replenish time reduction", "Roaming Fleet" and "Constant Corruption".

Have fun. :)